Hi! FirstReconstruction.py is initially meant to be called from the command line as it expects two command-line arguments (specified on line 7). When ran from a Jupyter Notebook (as in FirstReconstruction.ipynb), you need to manually provide values for sys.argv[1] (the output image) and sys.argv[2] (the geometry). Here, you script tries to write the image to an undefined place, producing the error. In RTK.ipynb, you did specify the "geometry" variable as a rtkFDKConeBeamReconstructionFilter, hence the error. It needs to be of type rtkThreeDCircularProjectionGeometry. Hope it helps! Aurélien. On Wed, 2020-04-22 at 11:33 +0900, 나윤호 wrote: > Here's my jupyter file. > I just found something strange. > > I'll send you two files. > > they both have same script in it but having different error. > > FirstReconstruction.ipynb is exactly same as the one in the github > example. > > and the other one is same except for the plotting of sinogram data > for practicing itk. > > I have no idea why they have different error > > > > 2020년 4월 21일 (화) 오후 10:22, Simon Rit <simon....@creatis.insa-lyon.fr> > 님이 작성: > > Please share your ipynb jupyter notebook file because I did the > > test with a new conda environment right now and it works for me... > > Thanks, > > Simon > > > > On Tue, Apr 21, 2020 at 10:41 AM 나윤호 <yoonho94...@gmail.com> wrote: > > > Before I run the script, I installed itk and itk-rtk using > > > pip.and then I copied > > > > > > and pasted > > > > > > the whole script in FirstReconstruction.py in a jupyter notebook > > > cell. > > > Do I need any additional installation to use rtk? > > > > > > Thank you for your answer of second question. > > > > > > 2020년 4월 21일 (화) 오후 5:27, Aurélien Coussat <aurelien.coussat@crea > > > tis.insa-lyon.fr>님이 작성: > > > > On Tue, 2020-04-21 at 17:15 +0900, 나윤호 wrote: > > > > > Thank you for replying. > > > > > I'm pretty sure that I haven't changed anything in the > > > > > example script. > > > > > What I just did is copy and paste and run it. > > > > > > > > What process did you follow in order to run it? Are you running > > > > it from a shell command line (as in "python > > > > FirstReconstruction.py") or from a Python command line (running > > > > "python" then copy-pasting everything) ? Could you provide the > > > > exact steps you followed in order to reproduce the problem? > > > > > and could you explain me how to translate(?) does documents > > > > > into pythonic way? > > > > > (I don't know much about Clang) > > > > > > > > > > for example, in the link you gave me it says > > > > > > > > > > rtk::FDKConeBeamReconstructionFilter< TInputImage, > > > > > TOutputImage, TFFTPrecision > Class Template Reference > > > > > > > > > > > > > > > I empirically know that in python I have to type something > > > > > like > > > > > > > > > > rtk.FDKConeBeamReconstructionFilter[InputImage, OutputImage, > > > > > FFTPrecision] > > > > > > > > > > > > > > > Am I right?? > > > > > > > > Almost, but your intuition is correct! From > > > > rtkFDKConeBeamReconstructionFilter header file (http://www.open > > > > rtk.org/Doxygen/rtkFDKConeBeamReconstructionFilter_8h_source.ht > > > > ml), you can see that default values are already provided for > > > > TOutputImage and TFFTPrecision. From Python's point of view > > > > only a single argument is therefore required (TInputImage). You > > > > can see an example of FDKConeBeamReconstructionFilter starting > > > > from the 65th line of FirstReconstruction.py. > > > > Good luck! > > > > Aurélien. > > > > > 2020년 4월 21일 (화) 오후 4:58, Aurélien Coussat <aurelien.coussat@ > > > > > creatis.insa-lyon.fr>님이 작성: > > > > > > Hi, > > > > > > Your first error is really strange. The "geometry" variable > > > > > > is supposed to be typed as > > > > > > rtkThreeDCircularProjectionGeometry (defined line 14), > > > > > > while according to your error message it is of type > > > > > > rtkFDKConeBeamReconstructionFilter. Are you sure you > > > > > > haven't somehow altered the example script? > > > > > > About your second question, you can use > > > > > > rtkFDKConeBeamReconstructionFilter and provide it a > > > > > > parallel geometry. See the documentation for more details : > > > > > > http://www.openrtk.org/Doxygen/classrtk_1_1FDKConeBeamRecon > > > > > > structionFilter.html. > > > > > > Don't hesitate if something remains unclear! > > > > > > Aurélien. > > > > > > On Tue, 2020-04-21 at 12:06 +0900, 나윤호 wrote: > > > > > > > Hi.I'm a newbie to ITK and RTK. > > > > > > > I'm currently using python not C++ > > > > > > > > > > > > > > > > > > > > > so I installed ITK package and RTK package using > > > > > > > > > > > > > > pip install itk > > > > > > > pip install itk-rtk > > > > > > > > > > > > > > using ITK seems OK, but I'm having difficulties with > > > > > > > RTK. > > > > > > > > > > > > > > When I run the ITK example code, It worked well. > > > > > > > but when I tried to run the FirstReconstruction.py in the > > > > > > > github, > > > > > > > error occurrs. > > > > > > > > > > > > > > > ----------------------------------------------------- > > > > > > > > ---------------------- > > > > > > > > AttributeError Traceback > > > > > > > > (most recent call last) > > > > > > > > <ipython-input-1-be2ee9c70d3d> in <module> > > > > > > > > 19 for x in range(0,numberOfProjections): > > > > > > > > 20 angle = firstAngle + x * angularArc / > > > > > > > > numberOfProjections > > > > > > > > ---> 21 geometry.AddProjection(sid,sdd,angle) > > > > > > > > 22 > > > > > > > > 23 # Writing the geometry to disk > > > > > > > > > > > > > > > > AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' > > > > > > > > object has no attribute 'AddProjection' > > > > > > > > > > > > > > How can I fix this problem? > > > > > > > > > > > > > > and I have another question. > > > > > > > I want the reconstruct the sinogram image to phantom. > > > > > > > > > > > > > > usually what I did was using skimage.transform.iradon(). > > > > > > > what should I use in RTK to do Inverse radon transform or > > > > > > > Filtered back projection method? > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Rtk-users mailing list > > > > > > > Rtk-users@public.kitware.com > > > > > > > https://public.kitware.com/mailman/listinfo/rtk-users > > > > > > _______________________________________________ > > > > > > Rtk-users mailing list > > > > > > Rtk-users@public.kitware.com > > > > > > https://public.kitware.com/mailman/listinfo/rtk-users > > >
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